Aftermath
by Barbra4317
Summary: So this is kind of my take on what happened after Skye betrays the team, what she goes through and how she can hopefully mend some bridges
1. Chapter 1

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

**CHAPTER 1: Hiding**

Skye felt horrible for what happened to Scorch, and what was worse was she was no longer trusted by the people who had somehow wormed their ways slowly into her heart. She always knew that May never really liked her but Fitzsimmons and A.C. had trusted her and she had betrayed that trust. And then there was Ward. She knew how hard it was for him to open up to her because it was just as hard for her to trust anyone. And she betrayed that trust and she was probably never going to get it back.

It had been five days since Coulson had given her the bracelet. Three since Skye had finally bucked up and made her rounds of apologies. And three days of Ward still ignoring her. They stopped training all together and whenever she came into a room that he was in he got up and left. Skye knew she deserved it. She betrayed his trust, but she was hoping to gain it back. The only problem was how do you gain back someone's trust if they aren't talking to you?

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It was a little after seven in the evening and Skye was hiding in her room, door shut. She couldn't bear to walk around the cabin when everyone on the plane hated her. She had gotten up once early in the morning before everyone got up to use the bathroom and grab a quick snack before ducking back in her room. She stayed there for the rest of the day holed up with a book about computers. She was reading about a new way of hacking when she heard a light tap on her door.

Skye grumbled a little bit wondering who on earth it would be and got off her bed, unlocked the door and opened it up just enough to see their face. It was Coulson.

"Hellllo" Skye said wondering what she could have possibly done wrong.

"You weren't at breakfast, lunch or dinner" he said simply and handed her a plate of spaghetti and a bottle of water.

"Ah, thanks, but I'm not hungry" Skye said moving to close the door again. Coulson's foot blocked it.

"Skye, you need to eat something"

"I have" Skye said. She knew she shouldn't be this blunt with him, after all he was trying to be nice—in a way—but she really wasn't hungry.

"Okay then" Coulson said and then walked back down the hallway.

Skye sighed and shut the door to her room. She knew she was being stupid, she had betrayed them and here Coulson was bringing her food because she was too chicken to go into the kitchen and she refused. She wanted things to go back to normal. But she knew that wasn't gonna happen anytime soon.

So first chapter…hope it's okay. Anyways let me know!


	2. Chapter 2

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

**CHAPTER 2: Leaving?**

Skye was feeling useless. It had been a week without electronics, and a week of being shunned by everyone on the plane. Okay so in reality it was just Ward who was ignoring her, Fitzsimmons were slowly starting to talk to her again. And AC at least stopped by once a day to check on her. But Ward was a different story, they had stopped work outs and whenever she entered a room he would leave and she couldn't take it anymore. She had heard over the loudspeakers that they were stopping at their main hanger where her van was for a few days break. Skye decided it was time to leave and get off the damn plane. She was able to; she was just a consultant, not even a real agent which they had made very clear. The only problem now was how to get the stupid bracelet off her wrist once she was gone.

Her plan was simple, once they landed ask for her van back, get the bracelet off and disappear. She was going to have to find a new van somewhere along the way and delete her history off of S.H.I.E.L.D. again. But she had done it before.

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When the plane landed Skye waited an hour before finally opening up her door. She ran down to the lab which to her relief was empty and found something to get her bracelet off. She clenched her teeth as it shocked her, but after a few minutes she managed to get it off. She grabbed her computer, deleting the video feed and then ran back to her room. She got onto the mainframe and deleted her history for what she hoped was the last time. Left her bracelet on the pillow and ran out.

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She had been on the road for three hours when she finally ditched her van in a little convenient store area. She hitched a ride with a family until they reached a bigger city. Skye didn't know exactly where she was headed, all she knew was that she needed to get far enough away that she wouldn't be on S.H.I.E.L.D.'s radar, if that was ever possible.

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Two days later Coulson and the team arrived back at the plane. Everyone was talking about what they did on their vacation. Ward had stayed nearby and had learned some new fighting techniques from Agent Romanoff. Coulson had met up with Agent Hill and Director Fury. Fitzsimmons had looked at all of S.H.I.E.L.D's new equipment and even May had a good time. She had done a lot of yoga and met up with an old friend from the past.

When they boarded the plane Coulson immediately felt something was off.

"Where's Skye?" he asked

"Probably already on board sir" Ward said in a tone that meant he really couldn't care less.

Coulson ran up the stairs and into the holocom room. On the screens lay a simple note.

_A.C.,_

_Thanks for letting me tag a long for as long as I did. But I think you and I both know that this wouldn't have worked out. Thanks for everything, especially for giving me a second chance even though I really didn't deserve it. Tell Fitzsimmons thanks as well for being nicer to me these past couple of days._

_Skye._

"FITZSIMMONS!" Coulson yelled.

Everyone ran into the Holocom room and stared at the message.

"Find her" he said

"Okay, all we need is to trace a signal on her bracelet…." Simmons said

"That's going to be hard" Ward said walking up.

"Why's that?" Coulson asked.

"Because it's right here" Ward said holding up the silver bracelet. "Found it on her bed."

"Damn it" Coulson said.

"Alright well we could always try her van, if she left she would have needed a way out so she must have taken her van."

"How did she even get the bracelet off?" Ward asked?

"I have an idea, check the video cameras starting with when we all left" Coulson said.

"Nothing.." Fitz said.

"But how much does that really mean? If she got the bracelet off she could have deleted the footage." Ward said.

"AH! I found her van!" Simmons said.

"Where is it?" Coulson asked

"It's at a convenient store about 3 hours from here." Said Fitz

"She ditched it sir, she must have known we had a tracker on it" Ward said.

"We don't know that for sure" Coulson said

"Coulson." May said nodding her head to the hallway.

"What? You don't think we should go after her do you?"

"It's obvious she wanted to leave. Besides it's for the better, We shouldn't have trusted not a real agent, just a consultant. I think it's time to cut our losses." She said.

"That's not right. She was a part of our team; she had access to some of our files, what if she leaks them?" Coulson asked hoping this would make May be on board.

"Then we'll find her. But right now, she doesn't want to be found." May said before turning on her heels heading back towards the cockpit.

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Thanks for the reviews hope you like this new chapter. PLEASE REVIEW!


	3. Chapter 3

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

**CHAPTER 3: Gone for Good**

Ward was pissed. She comes into their lives with her big brown eyes and he fell for it. And trusted her with something he doesn't trust anyone with. He had opened up a little bit and she betrayed him. He wanted to hate her. It would be easier to hate her for how she betrayed him. But he couldn't. He loved her which only made things that much more complicated.

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Skye laid across the bed of a creepy motel room in New Mexico it had been two weeks since she left the bus. She knew she needed to move on, but at the same time it was hard for her to keep moving. She wanted a family and she thought she had found it but she was wrong. She sighed and got into bed promising herself that she would buy a new van and head to somewhere she hoped they would never look for her.

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"Have we found anything on Skye?" Coulson asked. He missed her. She had grown on him and he missed her little quips and her sarcastic attitude. They needed her. Yeah the team was hurt that she had lied to them but with her gone the team had been different. They had changed they weren't laughing as much any more, even Fitzsimmons were quieter than normal. Skye was a huge part of the team and all of them were starting to regret their actions now that they were gone.

"Nothing sir, she's off the grid" Simmons said

"We do know that she was in Arizona but I don't think she's there anymore"

"Why do you say that?" Fitz asked

"I don't know it's just a feeling"

"Oh a feeling? That's great but that's not going to help us find her we need some sort of proof"

"I know but I can't find her! She's no where, she just vanished."

"Keep looking" a rough voice said.

They all turned around and were surprised to see Ward standing there, his arms crossed over his chest.

"Ward?" Fitz asked.

"Find her, she made our team better and we need to get her back to apologize and to hope she'll still be a part of our team. You were right sir." He said looking at Coulson. "She is beneficial to our team" he said then walked out.

"So…didn't see that coming" Fitz said looking at Simmons

"Oh please Fitz." Simmons said rolling her eyes as she went back to working.

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Skye got up early. Okay she told herself, time to go pick out your new home. But as she walked out of the room something or someone made her stop in her tracks.

It was Miles.

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AN: Hey sorry so I know this is a short chapter, but the next one is longer I promise! thank you thank you thank you for all of the awesome reviews. I'm so glad you're liking the story!


	4. Chapter 4

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

_Italics will be Skye's thoughts_

**CHAPTER 4: Miles**

"Miles?" Skye asked

"Hey Skye fancy seeing you around here"

"How the hell—" Skye started

"Don't worry about it Skye, but we need to talk" he said and then nodded his head towards a car which she presumed to be his.

_Okay Skye, you got this, it's just Miles. I mean you were boyfriend and girlfriend…kinda. He's not going to hurt you or anything._ Skye thought

"Okayy…about what?" Skye asked following Miles towards the car. She didn't get in however.

"Well how about we talk about S.H.I.E.L.D. I mean honestly what did they do to you after I was kicked off the plane?"

"They didn't do anything, I left on my own"

"Why didn't you contact me?"

"We broke up Miles, besides you have that bracelet that doesn't let you use electronics."

"Right, well I got someone else to do most of the hacking for me now" he said smiling.

"Oh? And Whose that?" Skye asked wondering who on earth would team up with him. All of the other hackers of The Rising Tide didn't really like him.

"You" he said before pulling out a taser.

The last thing Skye remembered was him leering over her body, and then darkness.

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"I can't believe there isn't a trace of her…" Simmons said sighing as she looked down at her tablet.

"Maybe she went back to—" Fitz started.

"No, no way she wouldn't have done that, I talked to her about it…before she left, and she would never go back to Miles. She hates him, he betrayed her."

"Yeah the same way she betrayed us" Fitz said darkly.

"I thought we agreed to get over it?" she said frowning. "We agreed that it was in the past, besides she was trying to make up for it. She apologized; I mean what else could she do really?"

"Yeah you're right" Fitz said sighing. "I just wish that none of this ever happened."

"Me too Fitz"

"Anything?" Ward asked gruffly walking in.

"Not so far, we just can't find her anywhere"

"What about friends, contacts? Come on she must have talked to someone." Ward said.

"I'm not really sure" said Simmons. "I mean after all she was living in a van when we found her. The other person, well he's got that bracelet on him so we'd be alerted if he used any electronics, which he hasn't which means he is most likely still where we left him." She said, avoiding Miles' name.

"It has a tracker though right?" Ward asked.

"Yes of course it does:" Fitz says. "Do you really think we would tag someone without—"

"Shut it!" Ward said frustrated. "Just run it, figure out where he is"

"On it" they said at the same time.

Ward rolled his eyes and walked up the staircase and headed towards Coulson's office.

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"Sir a moment?" Ward asked knocking on his door.

"Sure come in" Coulson said.

Ward walked in and noticed May standing on the other side of the room, arms crossed.

"I'm having Fitzsimmons run a trace on Mile's bracelet. Maybe we can ask him if he knows where Skye might go."

"Good thinking Ward" Coulson said.

Ward, getting the feeling that he walked in at a bad time nodded and then quickly left the room.

"Are we sure this is what we want?" May asked.

"Of course it is, our team is in chaos without her."

"Skye betrayed the team though" May pointed out.

"Everyone makes mistakes." He said.

"Yeah but—"

"Do you want to know why she joined us? Why she even hacked S.H.I.E.L.D. in the first place?" Coulson asked abruptly.

"Does it matter?"

"Yes" he replied quickly. May sighed and moved forward sitting in one of Coulson's chairs waiting.

"Skye doesn't know a lot about herself; she found as much as she could and then wiped herself completely from the cyber world."

"So?" May asked her face emotionless.

"So, her searches lead to this" Coulson said and then clicked his mouse. On the screen opened up the redacted file she had found. "She showed this to me before I gave her that bracelet. She doesn't know anything about her birth parents or where she came from, because of us. Because of S.H.I.E.L.D. and I want to know why. Now do you see why I gave her another chance?"

"Because you want to help her find her family?"

"No, I gave her another chance because everything she knows about family is that they leave her. Or it gets covered up by the government. I wanted to show her that we give second chances even if you do something wrong. That she belonged with us, and that if she proved herself, she could be a great asset, and maybe, we could help her figure out about her family."

May nodded her head.

"Er… excuse me Agent Coulson" Simmons' voice said tentatively over the intercom.

"Can you please come down here you're going to want to see this"

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AN: Thank you to the 48 people who are following my story! That is awesome, and thanks to the 22 favorites and 15 reviews keep it up! The quicker you review and the more people that follow the quicker I get things done! It's awesome that some of you figured out about the bracelet and it's ways of being a tracker…Thanks so much hoped you liked it. Please review!


	5. Chapter 5

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

_Italics will be Skye's thoughts_

**CHAPTER 5: Tell me Everything**

Coulson ran down to the lab area to find Fitzsimmons and Ward around the table.

"What is it?" he asked.

"Well, we found Miles"

"Okay? and where is he?" Coulson asked.

"He's in New Mexico"

"And you think Skye is there too?" Coulson asked

At the mention of Miles Ward's fingers clenched tightly in a fist, he couldn't believe that she met up with him again after everything. This new sting of betrayal hurt even more than the last and he was about ready throw something across the room.

"Why would she go to him I thought you said she wouldn't" Fitz asked looking at Simmons.

"That's just it, she wouldn't. She hated him; there is no way she would have gone back to him"

"Are you sure she wasn't just playing you?" Ward asked.

"I'm positive" Simmons said staring at him

"Okay, so what do we do?" Fitz asked

"We go find Miles, follow this lead and hopefully we figure out where Skye is" Coulson said.

"Well then" said May, all heads turned to look at her, none of them noticed her come in. "Planes already re-routing itself" she said looking pointedly at Coulson before heading back upstairs.

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Skye's head hurt. She couldn't figure out where she was exactly, but she was pretty sure she was in a storage container.

"Morning" Miles said looking up. "Glad you're finally awake"

"What do you want?" Skye snapped, or at least she tried to but she was still a little groggy so it didn't turn out as harsh as she wanted it to.

"What I want is for you, to set up this camera to stream a video online for the world to see. Since I'm not allowed to touch electronics"

Skye sighed and slowly got to her feet. Her entire body was sore. She slowly set up the computer to stream online and set the camera up facing a corner the opposite side of the storage container.

"Perfect" Miles said smiling. "Now I want you to take that remote, and sit in the chair. And when I tell you to, I want you to press the start button."

"What are you going to do?" Skye asked scared.

"Me? I'm not going to do anything, now my friend here…" he said opening the door of the container to let someone in…I can't say what he's going to do exactly."

Skye gulped. _Holy crap. _She thought. The man who came in was twice the size of Ward and about four times the size of her.

"What do you want?" She asked staring at the large man in front of her.

"What I want, is for you to tell me everything you know about S.H.I.E.L.D." he said.

"Shield? Like a knights shield?" Skye asked playing dumb.

"Shut up, I know you know all about it. Your boyfriend here told me all he knows already." He said roughly. "Now turn on the camera"

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The plane was still a good four hours away from New Mexico, and everyone on the team was doing their own thing. May was in the cockpit driving, even though she could put it on autopilot she didn't because she wanted sometime to think about everything Coulson had told her about Skye.

Coulson was sitting in his office going over all of the files Skye had shown him for what was probably the 100,000 time. Ward was sitting on the couch reading, but all he could think about was Skye and the fact that she probably betrayed them again.

Fitzsimmons was downstairs in the lab keeping a constant eye for anything 'Skye related' as well as forming a new experimental weapon. That's when they heard the ding on their computer.

"Holy crap!" Simmons said, and then ran over to the intercom hurriedly calling the team down to the lab again. Meanwhile, Fitz pressed the record button and they watched the screen in horror.

"What?" Ward asked rushing down to the lab, Coulson right behind him, and May a few seconds later.

"Look" Simmons said pointing to the screen.

They looked and were shocked to see an online video streaming live that had a grainy picture of Skye and a big mans back. Skye was tied to the chair her face looking up defiantly at him.

"Now, tell me everything you know about S.H.I.E.L.D." he said.

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AN: Wow guys thanks to you all there officially over 50 followers of this story! My way to say thanks is to post this new chapter Hope you liked it, and if you did please review!


	6. Chapter 6

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

PLEASE NOTE! I'M NOT SURE HOW RATINGS REALLY WORK, BUT THERE'S SOME TORTURE-Y STUFF IN THIS CHAPT. NOT TO HORRIBLE. PLS DON'T READ IF YOU DON'T LIKE THAT STUFF, YOU CAN SKIP THIS CHAPTER AND STILL UNDERSTAND WHAT'S GOING ON.

_Italics will be the voices in the video._

**CHAPTER 6: Help Her!**

The team stood their frozen as the large man loomed over Skye.

"_Now, tell me everything you know about S.H.I.E.L.D."the man said._

"_Shield? Like a warrior shield?" Skye asked playing dumb._

_The man reached out and struck her across the face._

"_Don't play dumb with me, Bitch. You used to stand for something, a part of the Rising Tide. You were one of their best hackers, helping them get the information out into the world as it should be. And here you are protecting them! Protecting government secrets, secrets which go against everything you ever fought for! Now come on help me share the news of what S.H.I.E.L.D. does to the rest of the world, like all information should. _

"_Go to hell" Skye said_

_The man hit her across the face again._

"_Okay, fine, I guess we're doing this the hard way. As S.H.I.E.L.D. has probably figured out by now, assuming that they're watching this that they can't figure out an exact location on where I am, which means no one is coming for you"_

"_I wouldn't expect them to anyways" Skye says_

"_If you don't expect them to come then why not tell me and the rest of the world everything you know?"_

"_Because it's wrong! I've been with them to realize that something's should be kept a secret to help protect the world! And AC if you're listening, it's Mile—"her words were cut off by a third, and then fourth blow to the face. Her head slumped slightly._

"_Stupid Bitch. Wake her up!" he yelled and then a black cloth was thrown over the camera lens.._

The team stood their stunned. The first to snap out of it was Coulson.

"Can we figure out where it's coming from?"

"No, not exactly, it is coming from somewhere in New Mexico; they are most likely bouncing off a free Wifi service like Skye did." Fitz said

"How long till we get there?" Ward asked

"At least 4 hours" May said looking at the black screen with distaste.

"That's too much time!" Ward said frustrated. "That guy is going to beat her till they find out what she knows! We have to help her!"

Coulson was just about to respond when the cloth was removed from the lens.

"_So Skye, as we were discussing let's talk about S.H.I.E.L.D. I already know that they have a plane for headquarters. That I learned from you're boyfriend Miles"_

"_He's not my boyfriend!" Skye yelled angrily "He betrayed me" _

"_But didn't S.H.I.E.L.D. betray you, otherwise why would you be out here all alone?" _

"_I chose to leave?" Skye mumbled_

"_Oh you chose to, and why's that?"_

"_It doesn't matter, what does matter is that I am never giving up S.H.I.E.L.D. besides I barely had any clearance there anyways" _

"_Tell me about your teams weak points. For instance, Jemma Simmons?"_

_Skye kept her mouth shut._

"_No?" The man said, before grabbing a small knife out of his pocket. _

"_No, please no! Please!" Skye said squirming in her seat. But it was too late; the man had lifted her shirt up and cut a horizontal line across her stomach. Skye screamed._

"Coulson! Please there has got to be something we can do!" Ward begged. He looked around and noticed that Coulson wasn't here anymore.

Ward looked back at the screen and noticed that blood was forming quickly, staining Skye's light blue shirt.

"_That's enough for one day, until next time" the man said facing the camera grinning behind his mask before turning off the camera. _He knew S.H.I.E.L.D. was watching and he couldn't wait to see what they'd do next. Them rescuing her would only prove that Skye was an asset to them and would hopefully help him show the world some of the true faces of S.H.I.E.L.D.'s agents as well as get a video of their airplane and the tech that S.H.I.E.L.D. had.

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After he saw the man grab a knife Coulson ran up the stairs pulling out his phone as he did. He called a familiar number in his phone and pressed send.

"I don't know who the hell this is, but you better tell me what the hell you're doing with Coulson's phone!" a voice yelled.

"Look, I can't explain right now, but I promise I will" Coulson said. "But right now I really need a favor" he said.

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AN: hmmm who do you think he called? And just so you know, this isn't bashing activists or anything like that. The character whose beating up Skye, I basically just made him a creepy psychopath who latched onto the ideas but isn't doing things in the right way.

Please Review!


	7. Chapter 7

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

**CHAPTER 7: I Can't Believe it's Him**

Skye was sore. She could feel her face swelling from the man hitting her, but what hurt the most were the cuts that he had made along her stomach. She felt herself starting to fall out of consciousness. She couldn't believe this was happening to her.

When she had been tied to the chair she knew it was going to be bad. She just didn't realize how bad it was going to be. But there was no way she was going to give up S.H.I.E.L.D. she already made the mistake of warning Miles and she wasn't about to make another mistake by telling the man what he wanted to know. She wanted to prove herself to them in a way. She wanted them to know that she could be a good asset. She had been given a second chance and this time she was going to prove herself to them. She was going to act like a good agent like Ward and not tell them anything no matter what they did to her. She tried to warn the team about who it was hoping they'd find her. But she wasn't sure if they would. She hoped.

Skye's eyes were growing heavy; she knew it was blood loss. She gulped, thinking she was going to die in this hell hole with Miles and the creepy man Miles befriended. Skye was fighting to stay conscious from the blood loss, she needed to stay awake. She needed to, she thought about Ward and how he would have been out of this mess by now, and Agent May wouldn't have even been in this situation in the first place. She tried to fight through the pain and began to twist her wrists trying to get out of the binds.

Then all of a sudden the door to the storage room opened and a ray of sunshine shone on her body. She closed her eyes, the sudden light hurt them, but around her she heard the sound of fighting. Skye leaned as far back in the chair as possible as she heard someone walking towards her, she tried to open her eyes but found she couldn't she was tired, the blood loss and pain finally taking over she finally let go and passed out not caring what happened to her anymore.

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"Where'd you go? He cut her! Several times! We have to get some agents to go down there" Ward said frustrated at Coulson who had just walked back into the lab.

"May, change flight directions, we're heading to New York."

"New York?" May asked confused.

"Yes" Coulson said calmly. May just nodded and headed up to the cockpit.

"Sir, if I may, Skye is in the opposite direction"

"Trust me, by the time we get to New York Skye will be there"

"That's impossible, we'll be to New York in like two hours, do you really expect us to believe that she will be there some how?" Fitz asked

"Yes I do" Coulson said

"How?" Ward asked

"That's classified for the time being"

"Are you kidding me!" Ward said frustrated from the secrets. He finally understood why Skye always got annoyed at S.H.I.E.L.D. for classifying things.

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Skye was feeling tired and yet oddly comfortable. The last thing she remembered was a man walking towards her. She opened her eyes and found herself in a bedroom. She tried to sit up when someone placed a hand on her shoulder.

"Lay down, you need your rest" a man said.

Skye looked to her right and nearly jumped out of her skin when she saw who was sitting in a chair next to the bed.

"Holy crap you- you're"

"Tony Stark" he said smirking.

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AN: I loved how many of you guessed who it was and was right! I know for some it was pretty obvious who Coulson was called. And I think in any situation its true like him and Stark were pretty dang close and so I think if Coulson would break 'regulations' and go to outside help it would be Stark. Anyways please review and lemme know what you thought!


	8. Chapter 8

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

**CHAPTER 8: Tony Freakin Stark**

"How long have I been here?" Skye asked staring at The Tony Stark

"About an hour, Coulson and his team will be here in about an hour" he said

Just then the door opened and a woman walked in.

"Hi, how are you feeling Skye?" Pepper asked.

"Umm…I'm fine…how do you know my name?" Skye asked

"Oh, Phil told us when he told us when he called." She said

"Wait AC called you?" Skye asked confused.

"Right, sorry sweetie" Pepper said walking over "This must be really confusing for you" Pepper said taking Skye's hand.

"Umm..." Skye said not really sure what she was supposed to say. Skye sat up a little in bed and looked around the room more.

"Basically…" Stark started "Coulson called and told us that one of his assets was kidnapped and was being tortured for information on S.H.I.E.L.D. and he couldn't get there fast enough and asked for my help. I looked at the video and realized you were in a storage container, and we already knew you were in New Mexico, and it was really easy after that, just hopped in my suit and used thermal imaging to find which container you were in"

"But there are billions of storage containers." Skye said still slightly confused on how he found her.

"True but first using—"he stared when Pepper cut him off.

"It doesn't really mater, what matters is that you're safe here. And luckily since the Battle of New York Tony here has been a little over protective of me" Pepper said looking at Stark "and he has a doctor who lives here and was able to set up an IV and stitch up the cuts on your stomach you should be back on your feet in a couple days, however you're going to be pretty sore."

Skye just looked dumbly at the pair of them.

"Come on Tony, we should let her get some rest and mull things over for a bit" Pepper said holding her hand out. Skye stared at the door after they left until fatigue won over and she fell back asleep.

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"How is she?" Coulson asked walking into Stark Towers with his team behind him.

"Wait wait you owe me an explanation how the hell are you not dead?" Stark asked

"I'll tell you everything after we see Skye" Coulson argued, he was not in the mood for his games right now he wanted to see Skye and make sure she was okay.

"She's fine Phil" said Pepper walking out from the kitchen. "She's resting right now"

Coulson nodded. "Thank you" Coulson said looking at Stark.

"You're welcome, so who is she to you guys?" He asked as they all moved into the living room sitting down on their couches.

"More importantly" Pepper said "Hi I'm Pepper Potts, who are all of you?" she asked looking at Coulson's team.

"Right sorry, Fitz ,Simmons, Agent Ward, and Agent May" Coulson said pointing them out to Pepper and Stark.

"Hi" They all said

"So, how are you alive?" Stark asked

"Fury thought—"Coulson started but was soon interrupted by another voice.

"AC?"

The team looked to their left and Skye walking slowly down the hallway towards them. Her hands on her stomach as she walked. They all held their breaths when they saw her face. Her face was swollen and she had a black eye on her right eye.

"Skye" Ward breathed.

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AN: Hope you liked it! Can I just say how freakin' excited I am for the new episode? It's going to be awesome! Poor Skye though, looks like she is butting heads with the agent of charge (no more than usual…) and May saying that Skye shouldn't be on the team? UGH!

Anyway Please review and lemme know your thoughts on the story or if you're just excited as I am about the new episode!


	9. Chapter 9

Aftermath:

Following the episode- A girl in a Flower Dress. My story will continue from there and eventually include the following episodes that air.

_Italics mean Stark's thoughts_

**CHAPTER 9: Skye's Story**

"Skye you really shouldn't be walking you were just stitched up an hour ago" Pepper said walking over to her. She helped Skye over to the couches and sat her next to Agent Ward. Pepper fought the urge to smile as she saw the way he looked at Skye as Pepper led her over to the couches.

"How are you Skye?" Coulson asked trying hard not to stare at the bruises on her face.

"I'm fine" She said trying to be cool about everything. Truth was her entire body hurt and she was thankful to Pepper for helping her over to the couches because she knew there was no way she would have made it over there without collapsing.

"Skye" Simmons said and got up from her spot and gently gave Skye a hug. "I'm so glad that you're back". Skye smiled and nodded.

Ward was fighting the urge to pull Skye into his side and never let her leave; silently he moved his hand and intertwined it with hers. He gave her hand a soft squeeze and when she looked up at him he offered her one of his rare smiles.

"I'm glad you're back rook" he said quietly so only she could hear. She smiled leaned against him slightly.

"So what happened Skye? Why'd you leave?" Fitz asked. Everyone looked at him rolling their eyes.

"Fitz!" Simmons said exasperatedly.

"What! We're all thinking it" he said defensively.

"Well…" Skye said awkwardly. "I just…there was a lot of tension on the bus after the whole Miles thing. And I know we were slowly starting to talk again" she said looking at Fitzsimmons and AC. "But it was hard and I just figured it would be easier if I was gone. I mean it wasn't like I was being any help on the bus. With that bracelet on me I wasn't allowed to use technology and that's all I'm really good at and Ward and I weren't talking…" she said pausing to look down at their now intertwined hands. "And I just thought, well I'm not being useful around here and I might as well leave. After I left I'm pretty sure you know I grabbed my van and drove. Ending up in New Mexico and I was going to head to the car dealership to buy a new car but before when I left my motel room I met Miles."

Ward's hand tightened as he heard Miles' name. His empty hand also curling into a fist.

"Anyways he tased me and when I woke up I was in that storage container" she said shuddering at the thought. "He wanted me to help him expose S.H.I.E.L.D. the way we had planned. With us getting the news out to the public like it should…But I didn't want to and then he made me set up the video camera because he couldn't touch electronics without you guys knowing. Anyways after he had me set it up the guy came in and sort of took things from there" she said not wanting to talk about what happened after that.

"Do you know who the man was?" Coulson asked.

"No, it's weird because Miles doesn't really have a lot of friends so I have no idea where he found him"

"Most likely it was some guy who was just paid to ask those questions and get you to spill everything you knew about S.H.I.E.L.D. if you wouldn't do it willingly."

"But why is Miles so focused on getting to S.H.I.E.L.D.?" Fitz asked confused.

"I can answer that one" Stark said from where he was sitting. Everyone looked at him surprised.

"Don't look so surprised" he said "From what I know, Skye you worked with The Rising Tide before joining up with S.H.I.E.L.D. and was dating him. Then when you guys met on that plane it became obvious to him that you had changed your mind about S.H.I.E.L.D. and about him. He blames S.H.I.E.L.D. for taking you from him. That's why he wanted to expose them so badly."

"Okay but why torture Skye? If he loved her he wouldn't want to hurt her right?" Ward asked

"He hoped that once she spilled everything she would realize who the real bad guy was in his mind, which is S.H.I.E.L.D. and then she would help him get his bracelet off and together they would hack S.H.I.E.L.D. and expose all of our agents and secrets that we have kept from the public." May said.

Skye looked at May shocked that was the most she had ever heard May speak.

"I don't think Miles meant for Skye to get hurt" May continued. "I think that was more of the man's idea…Miles wanted the information and I think the man took it as, any means necessary"

Ward squeezed Skye's hand again.

"Well what I want to know is how Miles knew where Skye was at all; I mean how did he know when we didn't know…" Coulson said…."But we can talk about it later"

"Well now that we have that settled, can you PLEASE tell me how the hell you're alive?" Stark asked. He knew he sounded rude, but at the same time he saw how uncomfortable Skye looked as they talked about what happened to her. _The least I can do is get their thoughts on something else for the time being. She doesn't need all of these questions right now. _

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AN: Hey all! I am so sorry I forgot to update on Tuesday, I was super busy and I was so excited for the episode which was amazing! I wont say anything about it incase someone didn't see it but if you have seen it lemme know what you thought about the secret that came out by reviewing! Hope you liked this chapter! Please please please review. I know Stark may sound like an ass a bit and not caring, but you have to remember he was effected a lot when Coulson died, and also I think in a way that Stark would do something like that for Skye.


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